Abstract

BACKGROUND:

The MHC, which is regarded as the most polymorphic region in the genomes of jawed vertebrates, plays a central role in the immune system by encoding various proteins involved in the immune response. The chicken MHC-B genomic region has a highly streamlined gene content compared to mammalian MHCs. Its core region includes genes encoding Class I and Class IIB molecules but is only ~92Kb in length. Sequences of other galliform MHCs show varying degrees of similarity as that of chicken. The black grouse (Tetrao tetrix) is a wild galliform bird species which is an important model in conservation genetics and ecology. We sequenced the black grouse core MHC-B region and combined this with available data from related species (chicken, turkey, gold pheasant and quail) to perform a comparative genomics study of the galliform MHC. This kind of analysis has previously been severely hampered by the lack of genomic information on avian MHC regions, and the galliformes is still the only bird lineage where such a comparison is possible.

RESULTS:

In this study, we present the complete genomic sequence of the MHC-B locus of black grouse, which is 88,390 bp long and contains 19 genes. It shows the same simplicity as, and almost perfect synteny with, the corresponding genomic region of chicken. We also use 454-transcriptome sequencing to verify expression in 17 of the black grouse MHC-B genes. Multiple sequence inversions of the TAPBP gene and TAP1-TAP2 gene block identify the recombination breakpoints near the BF and BLB genes. Some of the genes in the galliform MHC-B region also seem to have been affected by selective forces, as inferred from deviating phylogenetic signals and elevated rates of non-synonymous nucleotide substitutions.

CONCLUSIONS:

We conclude that there is large synteny between the MHC-B region of the black grouse and that of other galliform birds, but that some duplications and rearrangements have occurred within this lineage. The MHC-B sequence reported here will provide a valuable resource for future studies on the evolution of the avian MHC genes and on links between immunogenetics and ecology of black grouse.

Phylogenetic relationships of the coding sequences of the homologous genes in black grouse, chicken, turkey, quail and golden pheasant. The phylogenetic trees are constructed with the Neighbor-joining method. Numbers next to the branch points indicate the bootstrap values as percentages of 1000 replicates. The stars indicate the tree topology is the same as that of neutral makers.

Plotting of dN/dS values of MHC genes grouped by phylogenetic tree topology. One group includes the genes following the expected tree topology as neutral markers: TAPBP, BRD2, DMA, DMB1, BF1 and TAP2; the other includes the genes showing aberrant tree topology as neutral markers: Blec1, BLB1, BLB2, DMB2, TAP1 and BF2.